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There are three molecular mechanics methods available in Gaussian. They were implemented for use in ONIOM calculations, but they are also available as independent methods. No basis set keyword should be specified with these keywords.

The following force fields are available:

AMBER: The AMBER force field as described in [37]. The actual parameters (parm96.dat) have been updated slightly since the publication of this paper. We use this current version from the AMBER web site (amber.scripps.edu).

The surface data may be generated from a Gaussian checkpoint file or be read in from a cube file. Note that there are two steps involved in actually displaying a surface: Obtaining a cube by generating it or reading it in. Generating the actual surface for display. For those who don't want to read the entire document, I'll give a sneak peek at the essential point here; the rest of the document will be a description of how to create formatted checkpoint files and how to use them. GaussView gets results from Gaussian via formatted checkpoint files and log files (i.e. Gaussian output files). (Standard Gaussian input file extension is.gjf or.com.). If checkpoint file (. Chk) name is specified in the input as in the example. Read checkpoint file. The checkpoint file name. See Reading gaussian checkpoint files if you don't understand. Specify the type of density matrix you want; in the above it is the rohf type. You don't need to do an scf calculation, just specify the kind of density matrix in scfdata= Change the. Gaussian Tip: Finding out What's in a Checkpoint File Ever wonder what's in some of the numerous checkpoint files you have accumulated or which checkpoint file of several is the one you want? The chkchk utility will show you information about the job that created a checkpoint file.

DREIDING: The DREIDING force field as described in [38].

UFF: The UFF force field as described in [39].

CHARGE ASSIGNMENT-RELATED OPTIONS

Unless set in the molecule specification input, no charges are assigned to atoms by default when using any molecular mechanics force field. Options are available to estimate charges at the initial point using the QEq algorithm under control of the following options for any of the mechanics keywords:

QEq
Assign charges to all atoms using the QEq method [40].

UnTyped
Assign QEq charges only to those atoms for which the user did not specify a particular type in the input.

UnCharged
Assign QEq charges for all atoms which have charge zero (i.e., all atoms which were untyped or which were given a type but not a charge in the input).

PARAMETER PRECEDENCE OPTIONS

Terminology: Gaussian contains built-in parameter sets for the built-in force fields listed above; these are referred to as hard-wired parameters. Soft parameters are ones specified by the user in the input stream for the current job (or a previous job when reading parameters from the checkpoint file). By default, when no relevant option is given, the hard-wired parameters are the only ones used.

HardFirst
Read additional parameters from the input stream, with hard-wired parameters having priority over the read-in, soft ones. Hence, read-in parameters are used only if there is no corresponding hard-wired value. Note that wildcards matches within the hardwared parameter set take precidence over soft parameters, even when the latter contains an exact match for the same item. Use SoftFirst if you want to override hard-wired parameter matches.

SoftFirst
Read additional parameters from the input stream, with soft (read-in) parameters having priority over the hard-wired values.

SoftOnly
Read parameters from the input stream and use only them, ignoring hard-wired parameters.

ChkParameters
Read parameters from the checkpoint file. Any non-standard (soft) parameters present in the checkpoint file are used with higher priority than corresponding hard-wired parameters, unless HardFirst is also specified.

NewParameters
Ignore any parameters in the checkpoint file.

Modify
Read modifications and additions to the parameter set (after it has been constructed from hard and/or soft parameters).

HANDLING MULTIPLE PARAMETER SPECIFICATION MATCHES

Since parameters can be specified using wildcards, it is possible for more than one parameter specification to match a given structure. The default is to abort if there are any ambiguities in the force field. The following options specify other ways of dealing with multiple matches.

FirstEquiv If there are equivalent matches for a required parameter, use the first one found.

LastEquiv
If there are equivalent matches for a required parameter, use the last one found.

INPUT CONVENTIONS

AMBER calculations require that all atom types be explicitly specified using the usual notation within the normal molecule specification section:

Consult the AMBER paper [37] for definitions of atom types and their associated keywords.

Atom types and charges may also be provided for UFF and DREIDING calculations, but they are not required. For these methods, the program will attempt to determine atom types automatically.

Analytic energies, gradients, and frequencies.

ONIOM, Geom=Connect

GENERAL MOLECULAR MECHANICS FORCE FIELD SPECIFICATIONS

Unless otherwise indicated, distances are in Angstroms, angles are in degrees, energies are in Kcal/mol and charges are in atomic units. Function equivalencies to those found in standard force fields are indicated in parentheses. In equations, R refers to distances and θ refers to angles.

Wildcards may be used in any function definition. They are indicated by a 0 or an asterisk.

In MM force fields, the non-bonded (Vanderwaals and electrostatic) interactions are evaluated for every possible pair of atoms. However, interactions between pairs of atoms that are separated by three bonds or less are usually scaled down (in most force fields, using a factor 0.0 for pairs separated by one or two bonds, and some value between 0.0 and 1.0 for pairs that are separated by three bonds).

There are a number of ways to implement the calculation of non-bonded interactions. We follow a two-step procedure. First, we calculate the interactions between all pairs, without taking the scaling into account. In this step, we can use computationally efficient (linear scaling) algorithms. In the second step, we subtract out the contributions that should have been scaled, but were included in the first step. Since this involves only pairs that are close to each other based on the connectivity, the computer time for this step scales again linearly with the size of the system. Although at first sight it seems that too much work is done, the overall algorithm is the more efficient than the alternatives.

In the soft force field input, the NBDir function entry corresponds to the calculation of all the pairs, and the NBTerm entry is used for the subsequent subtraction of the individual pairs. However, to make things easier, you can specify just the non-bonded master function NonBon, which is automatically expanded into the actual functions NBDir and NBTerm during pre-processing.

Vanderwaals parameters, used for NBDir and NBTerm (See MMFF94 below for MMFF94-type Vanderwaals parameters).

VDWBond-length Well-depth

MMFF94 type Vanderwaals parameters (used for NBDir and NBTerm).

VDW94Atomic-pol NE Scale1 Scale2 DFlag

Atomic-pol Atomic polarizability (Angstrom³).
NE Slater-Kirkwood effective number of valence electrons (dimensionless).
Scale1 Scale factor (Angstrom^1/4).
Scale2 Scale factor (dimensionless).
DFlag 1.0 for donor type atom, 2.0 for acceptor type, otherwise 0.0.

MMFF94 electrostatic buffering

Buf94Atom-type Value

Non-bonded interaction master function. This function will be expanded into pairs and a direct function (NBDir and NBTerm) before evaluation of the MM energy.

NonBonV-Type C-Type, V-Cutoff C-Cutoff VScale1 VScale2 VScale3 CScale1 CScale2 CScale3

V-Type is the Vanderwaals type:
0 No Vanderwaals
1 Arithmetic (as for Dreiding)
2 Geometric (as for UFF)
3 Arithmetic (as for Amber)
4 MMFF94-type Vanderwaals
C-Type is the Coulomb type:
0 No Coulomb
1 1/R
2 1/R²
3 1/R buffered (MMFF94)
V-Cutoff and C-Cutoff are the Vanderwaals and Coulomb cutoffs (respectively):
0 No cutoff
>0 Hard cutoff
<0 Soft cutoff

VScale1-3 are Vanderwaals scale factors for 1 to 3 bond separated pairs. CScale1-3 are Coulomb scale factors for 1 to 3 bond separated pairs. If any scale factor < 0.0, the 1/1.2 scaling is used (as for Amber).

Coulomb and Vanderwaals direct (evaluated for all atom pairs).

NBDirV-Type C-Type V-Cutoff C-Cutoff

V-Type, C-Type, V-Cutoff, and C-Cutoff as above.

Coulomb and Vanderwaals single term cutoffs

NBTermAtom-type1 Atom-type2 V-Type C-Type V-Cutoff C-Cutoff V-Scale C-Scale

V-Type, C-Type, V-Cutoff, C-Cutoff, V-Scale, and C-Scale as above.

Atomic single bond radius

AtRadAtom-type Radius

Effective charge (UFF)

EffChgCharge

GMP Electronegativity (UFF)

EleNegValue

Step down table

TableOriginal-atom-type Stepping-down-type(s).

Harmonic stretch I (Amber [1]): ForceC*(R-Req)²

HrmStr1Atom-type1 Atom-type2 ForceC Req

ForceC Force constant
Req Equilibrium bond length

Harmonic stretch II (Dreiding [4a]): ForceC*[R-(R_i+R_j-Delta)]²

HrmStr2 Atom-type1 Atom-type2 ForceC Delta

ForceC Force constant
Delta Delta
R_i and R_j are atomic bond radii specified with AtRad.

Harmonic stretch III (UFF [1a]): k*(R-R_ij)²

Equilibrium bond length R_ij = (1 - PropC*lnBO)*(R_i + R_j) + R_en
Force constant: k = 664.12*Z_i*Z_j/(R_ij³)
Electronegativity correction: R_i*R_j*[Sqrt(X_i) - Sqrt(X_j)]²/(X_i*R_i + X_j*R_j)

HrmStr3Atom-type1 Atom-type2 BO PropC

BO Bond order (if <0, it is determined on-the-fly)
PropC Proportionality constant

R_i and R_j are atomic bond radii defined with AtRad. X_i and X_j are GMP electronegativity values defined with EleNeg. Z_i and Z_j are the effective atomic charges defined with EffChg.

Morse stretch I (Amber): DLim*(e^-a(R-Req)-1)² where a = Sqrt(ForceC/DLim)

MrsStr1 Atom-type1 Atom-type2 ForceC Req DLim

ForceC Force constant
Req Equilibrium bond length
DLim Dissociation limit

Morse stretch II (Dreiding [5a]): DLim*exp[-a(R_i+R_j-Delta)]-1)² where a = Sqrt(ForceC/DLim)

MrsStr2 Atom-type1 Atom-type2 ForceC Delta DLim

ForceC Force constant
Delta Delta
DLim Dissociation limit
R_i and R_j are atomic bond radii defined with AtRad.

Morse stretch III (UFF [1b]): A1*A3*(exp[-a(R-R_ij)]-1)² where a = Sqrt(k/[BO*PropC])

Equilibrium bond length R_ij = (1 - PropC*lnBO)*(R_i + R_j) + R_en
Force constant k = 664.12*Z_i*Z_j/R_ij³
Electronegativity correction: R_en = R_i*R_j*(Sqrt(X_i) - Sqrt(X_j))²/(X_i*R_i + X_j*R_j)

MrsStr3Atom-type1 Atom-type2 BO PropC

BO Bond order (if <0, it is determined on-the-fly)
PropC Proportionality constant

R_i and R_j are atomic bond radii defined with AtRad. X_i and X_j are GMP electronegativity values defined with EleNeg. Z_i and Z_j are the effective atomic charges defined with EffChg.

Quartic stretch I (MMFF94 [2]):

(Req/2)*(R-ForceC)²*[1+CStr*(R-ForceC+(7/12)*CStr²*(R-ForceC)²]

QStr1Atom-type1 Atom-type2 ForceC Req CStr

ForceC Force constant (md-Angstrom^-1)
Req Equilibrium bond length (Angstrom)
CStr Cubic stretch constant (Angstrom^-1)

Atomic torsional barrier for the oxygen column (UFF [16])

UFFVOx Barrier

Atomic sp3 torsional barrier (UFF [16])

UFFVsp3 Barrier

Atomic sp2 torsional barrier (UFF [17])

UFFVsp2 Barrier

Harmonic bend (Amber [1]): ForceC*(T-θeq)²

HrmBnd1 Atom-type1 Atom-type2 Atom-type3 ForceC θeq

ForceC Force constant (in kcal/(mol*rad²)
θeq Equilibrium angle

Harmonic Bend (Dreiding [10a]): [ForceC/sin(θeq²)]*(cos(θ)-cos(θeq))²

HrmBnd2 Atom-type1 Atom-type2 Atom-type3 ForceC θeq

ForceC Force constant
θeq Equilibrium angle

Dreiding Linear Bend (Dreiding [10c]): AForceC*(1+cos(θ))

LinBnd1 Atom-type1 Atom-type2 Atom-type3 ForceC

ForceC Force constant

UFF 3-term bend (UFF [11]):

k*(C0 + C1*cos(θ))+C2*cos(2θ) where C2=1/(4 * sin(θeq²)),
C1 = -4*C2*cos(θeq) and C0=C2*(2*cos(θeq²)+1)
Force constant: k = 664.12*Z_i*Z_k*(3*R_ij*R_jk*(1-cos(θeq²))-cos(θeq)*R_ik²)/R_ik⁵

UFFBnd3 Atom-type1 Atom-type2 Atom-type3 θeqBO₁₂BO₂₃PropC

θeq Equilibrium angle
BO₁₂ Bond order for Atom-type1–Atom-type2 (when <0, it is determined on-the-fly)
BO₂₃ Bond order for Atom-type2–Atom-type3 (when <0, it is determined on-the-fly)
PropC Proportionality constant

R_i, R_j and R_k are atomic bond radii defined with AtRad. X_i, X_j and X_k are GMP electronegativity defined with EleNeg. Z_i, Z_j and Z_k are effective atomic charges defined with EffChg.

UFF 2-term bend (UFF [10]): [k/(Per²)]*[1-cos(Per*θ)]

Force constant: k = 664.12*Z_i*Z_k*(3*R_ij*R_jk*(1-cos(Per²))-cos(Per)*R_ik²)/R_ik⁵

UFFBnd2 Atom-type1 Atom-type2 Atom-type3 Per BO₁₂BO₂₃PropC

Per Periodicity: 2 for linear, 3 for trigonal, 4 for square-planar.
BO₁₂ Bond order for Atom-type1–Atom-type2 (when <0, it is determined on-the-fly)
BO₂₃ Bond order for Atom-type2–Atom-type3 (when <0, it is determined on-the-fly)
PropC Proportionality constant

R_i, R_j and R_k are atomic bond radii defined with AtRad. X_i, X_j and X_k are GMP electronegativity defined with EleNeg. Z_i, Z_j and Z_k are effective atomic charges defined with EffChg.

Zero bend term: used in rare cases where a bend is zero. This term is needed for the program not to protest about undefined angles.

ZeroBndAtom-type1 Atom-type2 Atom-type3

Cubic bend I (MMFF94 [3]): (ForceC/2)*(1+CBend*(θ-θeq))*(θ-θeq)²

CubBnd1Atom-type1 Atom-type2 Atom-type3 ForceC θeqCBend

ForceC Force constant (in md*Angstrom/rad²)
θeq Equilibrium angle
CBend 'Cubic Bend' constant (in deg_-1)

MMFF94 Linear Bend (MMFF94 [4]): ForceC*(1+cos(θ))

LinBnd2Atom-type1 Atom-type2 Atom-type3 ForceC

ForceC Force constant (md)

Amber torsion (Amber [1]): Σ_i=1,4 (Mag_i*[1+cos(i*θ-I(i+4))])/NPaths

AmbTrsAtom-type1 A-type2 A-type3 A-type4 PO1 PO2 PO3 PO4 Mag₁Mag₂Mag₃Mag₄NPaths

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PO1-PO4 Phase offsets
Mag₁...Mag₄V/2 magnitudes
NPaths Number of paths (if < 0, determined on-the-fly).

Dreiding torsion (Dreiding [13]): V*[1-cos(Period*(θ-PO))]/(2*NPaths)

DreiTrsAtom-type1 Atom-type2 Atom-type3 Atom-type4 V PO Period NPaths

V Barrier height V
PO Phase offset
Period Periodicity
NPaths Number of paths (if < 0, determined on-the-fly).

UFF torsion with constant barrier height (UFF [15]): [V/2]*[1-cos(Period*PO)*cos(V*θ)]/NPaths

UFFTorC Atom-type1 Atom-type2 Atom-type3 Atom-type4 Period PO V NPaths

Period Periodicity
PO Phase offset
V Barrier height V
NPaths Number of paths. When zero or less, determined on-the-fly.

UFF torsion with bond order based barrier height (UFF [17]):

[V/2]*[1-cos(Period*PO)* cos(Period*θ)]/NPaths where V = 5*Sqrt(U_j*U_k)*[1+4.18*Log(BO₁₂)]

UFFTorB Atom-type1 Atom-type2 Atom-type3 Atom-type4 Period POBO₁₂NPaths

Period Periodicity
PO Phase offset
BO₁₂ Bond order for Atom-type1–Atom-type2 (when <0, it is determined on-the-fly)
NPaths Number of paths (when <0, it is determined on-the-fly)
U_j and U_k are atomic constants defined with UFFVsp2.

UFF torsion with atom type-based barrier height (UFF [16]):

[V/2]*[1-cos(Period*PO)* cos(Period*θ)]/NPaths where V=Sqrt(Vj*V_k)

UFFTor1Atom-type1 Atom-type2 Atom-type3 Atom-type4 Period PO NPaths

Period Periodicity
PO Phase offset
NPaths Number of paths. When zero or less, determined on-the-fly.
V_j and V_k are atomic constants defined with UFFVsp3.

UFF torsion with atom type based barrier height (UFF [16]) (differs from UFFTor1 in that the atomic parameter that is used): [V/2]*[1-cos(Period*PO)*cos(Period*θ)]/NPAths where V=Sqrt(V_j*V_k)

UFFTor2 Atom-type1 Atom-type2 Atom-type3 Atom-type4 Period PO NPaths

Period Periodicity
PO Phase offset
NPaths Number of paths. When zero or less, determined on-the-fly.

V_j and V_k are atomic constants from UFFVOx.

Dreiding special torsion for compatibility with Gaussian 98 code. During processing, it is replaced with DreiTRS, with the following parameters:

• If there are three atoms bonded to the third center and the fourth center is H, it is removed.

• If there are three atoms bonded to the third center, and at least one of them is H, but the fourth center is not H, then these values are used: V=4.0, PO=0.0, Period=3.0, and NPaths=-1.0.

• Otherwise, these values are used: V=1.0, PO=0.0, Period=6.0, and NPaths=-1.0.

OldTor Atom-type1 Atom-type2 Atom-type3 Atom-type4

Improper torsion (Amber [1]): Mag*[1+cos(Period*(θ-PO))]

ImpTrs Atom-type1 Atom-type2 Atom-type3 Atom-type4 Mag PO Period

Mag V/2 Magnitude
PO Phase offset
Period Periodicity

Three term Wilson angle (Dreiding [28c], UFF [19]): ForceC*(C1 + C2*cos(θ) + C3*cos(2θ)) averaged over all three Wilson angles θ.

WilsonAtom-type1 Atom-type2 Atom-type3 Atom-type4 ForceC C1 C2 C3

ForceC Force constant
C1, C2, C3 Coefficients

Harmonic Wilson angle (MMFF94 [6]): (ForceC/2)*(θ²) summed over all three Wilson angles θ.

HrmWilAtom-type1 Atom-type2 Atom-type3 Atom-type4 ForceC

ForceC Force constant

Stretch-bend I (MMFF94 [5]): (ForceC1*(R₁₂-Req₁₂)+ForceC2*(R₃₂-Req₂₃))*(θ-θeq)

StrBnd1Atom-type1 Atom-type2 Atom-type3 ForceC1 ForceC2 Req₁₂Req₂₃ θeq

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ForceC1, ForceC2 Force constants (in md/rad)
Req₁₂, Req₂₃Equilibrium bond lengths
θeq Equilibrium angle

USING SUBSTRUCTURES

Substructures may be used to define different parameter values for a function for distinct ranges of some geometrical characteristic. Substructure numbers are appended to the function name, separated by a hyphen (e.g., HrmStr-1, HrmStr-2 and so on).

The following substructures apply to functions related to bond stretches:

• -1 Single bond: 0.00 ≤ bond order < 1.50

• -2 Double bond: 1.50 ≤bond order < 2.50

• -3 Triple bond: bond order ≥ 2.50

The following substructures apply to functions for bond angles (values in degrees):

First substructure:

• -1 0 ≤ θ ≤ 45

• -2 45 < θ ≤ 135

• -3 135 < θ ≤ 180

Second substructure:

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• -i-n Number of atoms bonded to the central one.

For dihedral angles, one or two substructures may be used (e.g., AmbTrs-1-2). Use a zero for the first substructure to specify only the second substructure.

First substructure:

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• -0 Skip this substructure (substructure 'wildcard')

• -1 Single central bond: 0.00 ≤ bond order < 1.50

• -2 Double central bond: 1.50 ≤ bond order < 2.50

• -3 Triple central bond: bond order ≥ 2.50

Second substructure:

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• -i-1 Resonance central bond (1.30 ≤ bond order ≤ 1.70)

• -i-2 Amide central bond (priority over resonance)

• -i-3 None of the above

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Here is some simple MM force field definition input: